htslib
PostgreSQL
htslib | PostgreSQL | |
---|---|---|
7 | 409 | |
775 | 14,788 | |
1.5% | 2.3% | |
8.9 | 10.0 | |
5 days ago | about 12 hours ago | |
C | C | |
GNU General Public License v3.0 or later | GNU General Public License v3.0 or later |
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For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
htslib
- Gentoo -Os vs -O3 application startup time?
- Does anyone know of a repository for actual genetic data?
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Pigz: A parallel implementation of gzip for multi-core machines
There is another nice multi-core gzip based library called BGZF[1]. It is commonly used in bioinformatics. BGZF has the added advantage that it is block compressed with built in indexing method to permit seeking in compressed files.
[1] https://github.com/samtools/htslib
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Tips for scalable workflows on AWS
In contrast, processing can start immediately and only transfer what is necessary if tooling can read bytes of data directly from Amazon S3. Tools based on htslib can do this, so you can run something like:
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Software Development Project
Another idea is add in reading cloud data natively e.g. htslib which samtools relies on can read s3 directly. https://github.com/samtools/htslib
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Interested in Bioinformatics / C pair-programming opportunity / learning / portfolio project.
Greetings! I'm a bioinformatics software dev in San Francisco and I'm looking for others interested in working on a high-performance genetic data analysis project. The project is in C, using https://github.com/samtools/htslib.
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ffi-bitfield
I'm working on a bioinformatics-related binding called ruby-htslib. htslib makes heavy use of bit fields throughout the library, so supporting bit fields is inevitable.
PostgreSQL
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What do you want to watch next? This is why I built GoodWatch.
Data Handling: Utilizes Windmill for data pipelines, with a primary database powered by PostgreSQL. Auxiliary data storage is handled by MongoDB, with Redis for caching to optimize performance
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System Design: Databases and DBMS
PostgreSQL
- Presentación del Operador LMS Moodle
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Introducing LMS Moodle Operator
The LMS Moodle Operator serves as a meta-operator, orchestrating the deployment and management of Moodle instances in Kubernetes. It handles the entire stack required to run Moodle, including components like Postgres, Keydb, NFS-Ganesha, and Moodle itself. Each of these components has its own Kubernetes Operator, ensuring seamless integration and management.
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Integrate txtai with Postgres
Another key feature of txtai is being able to quickly move from prototyping to production. This article will demonstrate how txtai can integrate with Postgres, a powerful, production-ready and open source object-relational database system. After txtai persists content to Postgres, we'll show it can be directly queried with SQL from any Postgres client
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Understanding SQL vs. NoSQL Databases: A Beginner's Guide
SQL (Structured Query Language) databases are relational databases. They organize data into tables with rows and columns, and they use SQL for querying and managing data. Examples include MySQL, PostgreSQL, and SQLite.
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From zero to hero: using SQL databases in Node.js made easy
Node.js, MySQL and PostgreSQL servers installed on your machine
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I Deployed My Own Cute Lil’ Private Internet (a.k.a. VPC)
Each app’s front end is built with Qwik and uses Tailwind for styling. The server-side is powered by Qwik City (Qwik’s official meta-framework) and runs on Node.js hosted on a shared Linode VPS. The apps also use PM2 for process management and Caddy as a reverse proxy and SSL provisioner. The data is stored in a PostgreSQL database that also runs on a shared Linode VPS. The apps interact with the database using Drizzle, an Object-Relational Mapper (ORM) for JavaScript. The entire infrastructure for both apps is managed with Terraform using the Terraform Linode provider, which was new to me, but made provisioning and destroying infrastructure really fast and easy (once I learned how it all worked).
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How to dump and restore a Postgres DB with new table ownership
I've used MySQL for years. But recently, I found myself working PostgreSQL and simple things like dumping and restoring a database are different enough that I decided to document the process. It's straightforward enough once I knew how.
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Test Driving a Rails API - Part One
A running Rails application needs a database to connect to. You may already have your database of choice installed, but if not, I recommend PostgreSQL, or Postgres for short. On a Mac, probably the easiest way to install it is with Posrgres.app. Another option, the one I prefer, is to use Homebrew. With Homebrew installed, this command will install PostgreSQL version 16 along with libpq:
What are some alternatives?
genozip - A modern compressor for genomic files (FASTQ, SAM/BAM/CRAM, VCF, FASTA, GFF/GTF/GVF, 23andMe...), up to 5x better than gzip and faster too
psycopg2 - PostgreSQL database adapter for the Python programming language
seqtk - Toolkit for processing sequences in FASTA/Q formats
ClickHouse - ClickHouse® is a free analytics DBMS for big data
bwa-mem2 - The next version of bwa-mem
phpMyAdmin - A web interface for MySQL and MariaDB
cyvcf2 - cython + htslib == fast VCF and BCF processing
Firebird - FB/Java plugin for Firebird
aws-genomics-workflows - Genomics Workflows on AWS
Adminer - Database management in a single PHP file
libdna - ♥ Essential Functions for DNA Manipulation
SQLAlchemy - The Database Toolkit for Python